AninditaVarshneya BIOL368 Week 11

Contents

Purpose

To find out more information about the types of amino acid mutations between clones, and the structural impacts those mutations might have.

Methods and Results

Clones from visit 1 and 4 were uploaded to Biology Workbench, Protein Tools

Upload Huang protein sequence as well

Select all clones from a single subject as well as the Huang protein sequence

Run ClustalW Multiple Alignment and import the alignment into the Alignment Tools section

Select the alignment under Alignment Tools and run BoxShade

Open the Huang protein structure file on Cn3D, as well as the amino acid sequence

Select all amino acids of interest to analyze their importance in the structure of the protein. Using the space-filling model is helpful.

Highlight all amino acids in Cn3D that have corresponding amino acids in BoxShade that are not green

Highlight only amino acids with grayed out mutations, not including Huang

Highlight only amino acids with more than one grayed out mutations, not including Huang

Repeat these steps to analyze mutations in all other subjects against the Huang reference strain

After completing this work, my lab partner and I worked on our presentation for the following week (linked below).

Conclusion

Through structural analysis, I found that subjects from the moderate progressor group had significantly more amino acid substitutions along the surface of the gp120 protein compared to subjects from the rapid progressor group. Furthermore, I found that subject 14 has a single amino acid that multiple clones mutated. This was of especial interest to us because this amino acid was at a structural location that indicates that it interacts with the antibody proteins to some extent. While the extent of that interaction is unknown, the major mutations occurring at that place would affect the way gp120 sits in relation to the antibody. Furthermore, through research Matt and I found position 317 is a highly variant amino acid that also exists within the binding site for the antibody. This is interesting to us because we found that both subjects in the moderate progressor group had mutations in this region. Because it is within the binding site, mutations here would greatly affect the proteins ability to bind with the antibody. Considering the fact that this mutation was only found among moderate progressors, we can assume that, to a certain extent, the gp120 protein in moderate progressors did not bind with the antibody the same way that the gp120 protein in rapid progressors did. This means that the mutations we found in position 317 could represent some level of importance in the progression of HIV-1.

Acknowledgements

Matt Allegretti and I met to work on our research product during lab on 11/8/16 and again on 11/12/16 for several hours. We also worked on our research presentation together over Google Drive throughout the week. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.